The publication of documents outlining the risks relating to the government's health changes could lead to a "distorted and wildly speculative interpretation of risk", according to the permanent secretary of the Department of Health.

Una O'Brien also warned that publishing the documents would have a "chilling effect" on the way civil servants tasked with outlining the potential pitfalls of a policy commit their views to paper, as the government fights to keep secret the contents of its risk assessments of the government's shakeup of the NHS.

O'Brien was giving evidence to the information rights tribunal as the government seeks to overturn a November ruling by the information commissioner, Christopher Graham, who ordered the health secretary, Andrew Lansley, to release his department's risk assessment of the potential dangers of his radical shakeup.

It follows two separate freedom of information (FoI) requests lodged more than a year ago for the strategic risk register (February 2011) and the transition programme risk register (November 2010) to be made public.

Graham said in his ruling that disclosure of the two documents would significantly aid public understanding of risks related to the proposed changes and it would also inform participation in the debate about the reorganisation.

John Healey, the former shadow health secretary who submitted an FoI for the transition risk register, will say in his statement to the appeal tribunal that amid widening opposition to the legislative plan "the need for reassurance about the possible consequences" of the shakeup is "greater now than when I made my disclosure request".

But O'Brien spelt out her "deep concerns" that if the contents of the registers were made public at this stage, it would remove the "safe space" in which civil servants could be frank to ministers about the worst case scenarios of a given policy.

She said that while her instinct was to provide information, there needed to be a relationship of trust between civil servants and ministers where they were confident their assessments would not be disclosed.

Her "subsidiary" concern was that the contents of the documents "might be interpreted and mispresented".

She said risk registers were "living documents" that presented a snapshot in time that changed as the policy was developed, and warned that "if taken out of context, my own judgment is that they would lead to a distorted and wildly speculative interpretation of risk".

Her comments were backed by Lord O'Donnell, the former cabinet secretary, who said that the risk registers were by nature asymmetric because they were designed to guide policymakers to think about the various aspects of improving the policy.

O'Donnell, who retired in December, said: "It will understate the probability of very good outcomes … and it will overstate in people's minds the probability of very bad outcomes because the whole point of a scenario and analysis that you do is to think about the unthinkable." He said the registers were put together at a very early stage and were littered with red, in reference to the traffic light system of risk levels applied. But he said this was as it should be. "In fact, if you're going for a big reform programme, if it didn't have a whole series of reds, I would say there is almost certainly something with that risk register, by definition."

Had the documents been published, he warned that it would have adversely affected the public debate.

"There are very very strong public interest reasons for a department like health being able to formulate its policy the best it can," he said. "And when the permanent secretary tells you that actually with disclosing these risk registers we would end up with a worse policy that worries me."

Last month a Labour motion calling on ministers to release the risk register associated with the health and social care bill was defeated in the Commons. Shadow health secretary Andy Burnham told the Commons last month that the regional and local risk registers, which have been published, were "appalling and shocking". Some of the regional risk registers "predict poorer treatment for cancer patients", he said.

Burnham told MPs: "If this is what is published in local risk registers, it begs the question what on earth are they trying to hide in the national assessment? The simple truth is this: they can't publish because if people knew the full facts it would demolish any residual support that this reorganisation might have."

But he was criticised during the debate after it emerged that he had opposed the publication of a risk register while he was health secretary.